Speaking outside court in Pretoria after the withdrawal of the charges, Gen Khumalo expressed relief that the "truth at least is out".
Prosecutors had claimed that Dineo Mokwele was unqualified for the senior technical support services position she held within crime intelligence and labelled her a "token appointment".
Her appointment then came under scrutiny at the Madlanga Commission.
It heard that Mokwele was more than qualified for the post and had about a dozen certificates to her name.
In July, Andrea Johnson - the former head of a specialised unit within the National Prosecuting Authority (NPA) tasked with investigating high level and complex corruption cases - appeared before the commission.
She admitted that she was unaware of Mokwele's qualifications and apologised for remarks made about her.
Gen Khumalo became the head of Crime Intelligence in 2022. Up until then, he had served in different police units for more than two decades.
